On 1/17/13 1:24 PM, James Starlight wrote:
In addition to LINCS warning during last simulation I obtained the
next warning from mdrun (again that was when calmodulin reached close
compact conformation)
WARNING: Listed nonbonded interaction between particles 1230 and 1249
at distance 3f which is larger than the table limit 3f nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
what does it mean and how I could avoid it ?
Note the "IMPORTANT" statement. Your system is blowing up. Whatever you're
doing is causing the physical model to fail.
-Justin
2013/1/17 James Starlight <jmsstarli...@gmail.com>:
Dear Gromacs Users!
I'm simulatting open to close transition of calmodulin by means of
essential dynamics sampling. When my protein reaches closed state
(this time both ef hands domains aproach each other) I've obtain set
of lincs warnings and my simulatting crashes. I'm using gpu-based
gromacs with the sd integrator (As the thermostat). Below you can see
parameters for lincs options
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
Does it possible to resolve such problem by means of modification of
lincs options in mdp file ?
James
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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